The goal of the Epigenetics Core is to provide a robust common platform for the identification and analysis of genes affected by ethanol exposure, in the brain. The proposed RNA-seq and ChlP-seq studies will allow CARE Research Projects to obtain novel information regarding genome-wide changes in gene expression and in histone acetylation (the acH3K9 epigenetic mark). Results from these studies will provide a broader view of brain region-selective changes in genes that are likely to contribute to downstream plastic changes that accompany alcohol use and withdrawal. In Aim 1, the Core will analyze the rat brain transcriptome (by RNA-seq) in each of the three paradigms used in Projects 1-3: control liquid diet, chronic ethanol and withdrawal from ethanol. This will be performed on tissue dissected from selected brain regions including: the ventral tegmental area (VTA, Project 1), the amygdala (Project 2) and the hippocampus (Project 3). RNA libraries (3 reps per brain region per paradigm) will be prepared and sequenced using high-throughput technologies (lllumina). In Aim 2, the Core will perform chromatin immunoprecipitation (ChIP) using antibodies against a histone modification associated with active gene transcription (acetyl histone 3-lysine 9, acH3K9) for use in ChlP-seq assays. We will obtain and cross-link tissue corresponding to each paradigm and brain area as indicated in Aim 1. In Aim 3, both RNA-seq and ChlP-seq data will be analyzed by the High-Performance Biological Computing Group (Dr. Victor Jongeneel). The sequence data will be aligned to the rat reference genome and peaks called (for ChlP-seq) or expression of individual genes evaluated (RNAseq). Each treatment group and brain region will be independently analyzed and compared. Genes induced by alcohol exposure or withdrawal will be identified, and the pathways in which they participate analyzed. Target genes associated with synaptic plasticity that show changes in RNA levels as well as in acH3K9 will be selected for validation using either real time qRT-PCR or ChlP-PCR by the Epigenetics Core. The Core will train personnel from each CARE Project in the epigenetic assays outlined above.